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CHEM 184/284 (Chemical Literature) - Huber - Winter 2024: Lecture 9: Citations, Part II - Creating and Managing Them, EndNote Web

A two-credit course in the techniques and tools for effective searching the literature of chemistry, biochemistry, chemical engineering and related fields.

Citation Management

Citation -Why It is So Important in Scholarly Publishing

  • Anyone writing a scholarly paper - from a three-page paper for a freshman writing class, to a 500-page doctoral dissertation - is expected to properly cite his or her sources.  That means, providing in clear and understandable fashion, the information that a reader of the paper would need to track down that source material.  for example, citing a printed journal article, one should provide the author(s) name(s), the article title, the journal title, volume, issue, date of publication and page numbers.
  • But why is this expected?
    1. Attribution - If you have used information from someone else, you are expected to give the original source credit.  Not to do so, even if the original source is in the public domain, is plagiarism, a serious ethical offense in the scholarly world.  You would be, in effect, taking credit for someone else's hard work.  Moreover, how often a person's work is cited is considered a valuable measure of its importance to its field of research.
    2. Verification - If you have used information which is not completely presented in your paper, the reader must be able to go back and check the original sources, both to see whether you have reported the information accurately and to check how the original source gathered the information.
    3. Searchability - While this may not be important for that three-page freshman paper, most scholarly authors want to maximize the likelihood that others working in their field will be able to discover their work.  With the existence of databases whch index cited references (see below), a proper citation of a relevent source can mean that other scholars seeking to find papers which build on that previous research will find your paper.
  • An interesting point-of-view on the ethics of citations and their uses is Prof. Jan Reedijk's editorial in Angewandte Chemie International Edition, "Citations and Ethics"
  • Proper citation requires adherence to a consistent citation style.

Citation Styles

  • In order to ensure that all the necessary information to identify and locate cited references is provided by authors, publishers (and instructors in university courses, and departments receiving theses and dissertations!) will generally stipulate what citation style they wish their authors to follow. 
  • There are dozens of different citation styles, varying in popularity depending on the subject area involved. Most will require the same types of information, but may differ in detail, and may differ significantly in the order the information in which the information is arranged.
  • The UCSB Library provides a handy guide for major citation styles: Citation Styles at
  • Far and away the most important citation style for chemistry is the American Chemical Society's contained in the ACS Guide to Scholarly Communication.. ACS members can log in with their ACS ID and password. Also,, the ACS Style Quick Guide  is an open access chapter of the Guude. It is followed absolutely by ACS journals, and widely used by other chemistry publications as well. Note that the older ACS Style Guide, 3rd edition is still available online  Not all journals have switched over to the newer guide.
  • Other inportant science style guides include the Council of Science Editors manual, Scientific Style and Format, widely used in biology journals, and the National Library of Medicine's style guide, Citing Medicine, which is widely used in medical journals.  You can find links to information on these citation styles on the CSE/ACS/NLM page at
  • In some cases, style guides will require that cited journal names be abbreviated, which can pose a challenge both to the citing authro and to the reader attempting to track down a desired reference.  The most common abbreviation scheme used in chemistry is the one provided by Chemical Abstracts Service.  CAS now makes available a free online tool,   the CAS Source Index (CASSI) Search Tool at

Personal Bibliographic Software (PBS)

  • While keeping track of references and generating a properly formatted bibliography may be easy for a five-page paper, tracing years woth of references for a thesis, dissertation, review article, etc.  can be a major task.  In the old days, researchers might maintain file cabinets full of preprints and photocopied journal articles, with an index card file or typed list to keep track of them all.  And each time a new bibliography was needed for a new paper,, out would come the files and the work would be done over again.
  • In an era when nearly all literature searching is done electronically, and the vast majority of source documents (journal articles, patents, etc.) are received in electronic form, it makes sense that there should be ways to manage this data electronically too.
  • Today, sophisticated personal bibliographic software packages exist for both Windows and Macintosh personal computers. They not only store and retrieve lists of references, but you can import answer sets from indexing databases, and can format them according to a wide range of style guides, and generate bibliograpies.
  • Note that we are not talking here about database packages designed for the storage and retrieval of chemical structures and data (e.g. ChemBase, Isentris and the like). Those are beyond the scope of this course.

Desktop PBS

  • The first PBS systems were based on standard database software for personal computers, with customization to accomodate bibliographic data fields, and output to bibliographies according to particular citation styles.
  • Modern desktop PBS software can be extemely powerful and sophisticated.  Among such packages are:
    • EndNote ( from Clarivate Analytics, publishers of Web of Science. EndNote is available for both Windows and Mac OS, and is tightly integrated with Weo of Science, ResearcherID and EndNote online (see below.)
    • Papyrus ( was developed for the Macintosh, and became very popular among Mac PBS users, later adding a Windows version.  Papyrus is no longer being updated, but the last versions of each are available free of charge at the website.
    • Zotero ( is a free bibliographic software tool.  It was originally developed (and is still available) as a plug-in for the Firefox web browser.  It is now also available as standalone software for Windows, Mac or Linux, which can connect to Firefox, Safari or Chrome web browsers.  It is designed to pluck bibliograpic information directly from the browser screen. Fore more informatio about using Zotero, see the Zotero Workhop buide by Annie Platoff at
    •  For a large, if not comprehensive list of PBS packages and sites, see the Wikipedia article on comparison of reference management software at

Web-based PBS

  • In recent years, a variety of personal bibliographic tools have become available which store the database files on central servers, accessed through the Web.
  • Traditional-style PBS sites include:
    • RefWorks (  RefWorks is produced by ProQuest, and, unsurprisingly, is well integrated with ProQuest databases.  It requires either an individual subscription, or access to an institutional subscription.  UCSB does not have a RefWorks subscription at this time.
    • Zotero ( is a non-profit service, free to use, with features to let you collect, organize, cite and share your references.  One of its most imporant and useful features is a plug-in htat lets you collect references directly from your browser screen, whether from databases, full text journals online or webpages.
    • EndNote online (  Like the desktop EndNote, EndNote online is produced by Clarivate Analytics, and closely integrated with the desktop product, with the Web of Science platform and with ResearcherID.  EndNote online is available free to all users with registration. (UCSB has access as part of the UC Web of Science subscription to a somewhat enhanced version, including UC-e-Links embedded in document records.)  Purchasers of desktop EndNote also receive an EndNote online account.  EndNote online is described in much greater detail below.
    • Zotero - see above.
    • Mendeley ( Mendeley is a free tool now owned by Reed Elsevier, publisher of scholarly books, journals and satabases including Scopus.  It requires the download of software (Windows, Mac and Linux compatible), and stores both bibliographic references and electronic documents on a central server.  In addition to the tradtional PBS functions, Mendeley also acts as a scholarly social network, enabling the user to share references, annotations and collaborate with other Mendeley users.  Mendeley also now as an iPhone app for mobile users. It is now a subsidiary of Reed Elsevier, and cooperates tightly with their Scopus database and ScienceDirect full text collections..They have recently added the reference manager linked to above, andMendeley Cite, a downloadable app for adding citations from your Mendeley database to Microsoft Word documents.

© 20234Charles F. Huber

Creative Commons License
This work by Charles F. Huber is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
Based on a work at

Screenshots from EndNote online are copyright © 2018 by Clarivate Analytics.  Screenshots from Microsoft Word are © 2015 by the Microsoft Corporation.  All are used under fair use for educational purposes only.

EndNote (

The online version of EndNote, while significantly less sophisticated and powerful than the parent EndNote desktop software has the advantage of being free to any user, (Note: Institutional subscribers to Web of Science obtain access to a somewhat more powerful version.) and so a reasonable choice for students and others who may not need all the features but would like to use a PBS package, and, since it is based on Thomson's servers you can access it anywhere on any computer connected to the Web. Moreover, it is a very useful tool for collaborative research efforts: multiple users can share libraries of references, and cooperatively edit Word documents.

In addition to the information below, you may wish to consult some of the excellent online tutorials at provided by Clarivate Analytics. Tutorials are available in a variety of formats (including MP4 and WMV), and require a current Flash player for viewing.  You may also want to look at the EndNote Web help pages ( and the UCSB Library's guide to EndNote ( and the PDF guide to EndNote Web.

Creating an EndNote online account

  • Note that an account created for EndNote online also serves as an account for ISI's Web of Science databases (e.g. Web of Science, BIOSIS) for saving searches and setting up alerts and as an account for ResearcherID, and vice versa. Note, too, that EndNote online has very specific requirements for the number and type of characters in a password.
  • From the login screen (see below), if you are not already registered, click on the  Sign up link and follow the instructions.  If already registered, just log in.  (Note: UCSB does not yet have Shibboleth identity verification set up.  When we do, you would be able to log in using your UCSBnetID and password.)
  • You will first be prompted to enter and confirm an e-mail account.  Note that you do not need to use a UCSB e-mail account; indeed, if you want to keep the same EndNote account after graduation, you are better off using a commercial e-mail account. If you have already created an account using that e-mail, you will be notified, and prompted to login or reset your password.
  • Note that you can both sign up and log in  using a Facebook or LinkedIn account.  Your EndNote account will then be connected to the email address you used on that account.

EndNote web login screen


The EndNote online library screen

  • Here's an example (below) of the screen displayed after login, for a user who already has some collected references.
  • In the band at top, there is a "Welcome, <user's first name>" message, links to Web of Science, ResearcherID, Welcome *User* and Help.
  • Below that, there are tabs for the different functions of EndNote Web: My References (the opening default screen), Collect, Organize, Format, Match and Options. Further right are tabs for Connect, the online EndNOte user community, and Adminstrator Options.
  • On the My References screen, note the panel at left which allows you to select which group of references you wish to display, and to do a quick search of the references.  Note that if you have used ResearcherID to identify articles you have authored, the ResearcherID groups are listed there.
  • In the body of the screen, the brief records in the group are displayed.  One dropdown menu allows you to control the number of records displayed per page; another allows you to control the sort order (default is alphabetical by First Author; others are Year (of publication), Title, Source Title, Times Cited, date Added to Library and date Last Updated. Other links allow you to move between screens.
  • Each brief record displays the first author, year of publication, document title (linked to the full record), journal name (if applicable), the date the record was added to the EndNote library, and the date it was last updated, a link to the Web of Science record for the item (if available), and, for UC users, a UC-e-Links button. Note: if off campus, log into the Off-Campus Access (proxy server) before goint to EndNote to make best use of this feature.


EndNote online opening screen


  • Looking at the opening screen above:
    • Top right - Clicking on the grid opens a dropdown menu of links to other Clarivate resources: Web of Science, ResearcherID and Publons (discussed below). Clicking on the human figure icon gives you access to your account profilepolicy informationHelpFeedback, and log out.
    • Menu bar. From left to right:
      • My References - displays your list of groups, including, All my Referenes and Unfiled. The references in whichever group you have selected will be displayed. (Note that when you are just starting out, no groups or references will be displayed.)
      • Collect - when you hover over or click on this link, you'll see a list of options for brining references into your EndNote database (see below)
      • Organize - Hovering over or clicking on this link displays options for organizing your collected references, such as managing your groups (see below.)
      • Format - This link gives you options for creating bibliographies in your chosen citation style, and exporting references. (see below)
      • Match - This is a tool for locating suitable journals in which to publish a given paper (see below)
      • Options - Manage your settings and profile information
      • Downloads - Click on this link to get access to three tools: CiteWhileUWriteCapture Reference, and EndNote Click. Each will be explained below.
  • On the left side of the creen is the list of your groups, with a search window, in which you can search for a reference within any specified group or all of them.
  • Below is an example of a references list.

EndNote references list screen

  • Above the list is a drop-down menu allowing you to select how many references display on a page: 10, 25 or 50. To the right of that is a navigation tool allowing you to page through the displayed group of references, or jump to first, last or selected by number pages.
  • You may select references by clicking the check box to the far lest of the reference record, or you may select the entire page, or the entire group by clicking the appropriate check box above the list. You maay tnen add the selected records to an existing group, or create a new group, or add them to the Quick List, or delete them. Note that you may have the same record in multiple groups if you so desire.
  • Note that, as a UC user, there are Get it at UC links attached to each record.
  • Note the Authors, Date and Title headings above the list. By clicking on the heading, you can sort the list by that field. Click again to switch from ascending to descending order or vice versa. You can also use the drop-down menu on the right hand side to sort by First Author, Year, Title, Source Title, Times Cited, Added to Library, or Last Update in either order.
  • In the list itself, note that the first author (where available), publication date (where available) and document title are displayed. Beneath the document title are dates added and updated,links to outside sources and attached documents (if any). If you are viewing your list through a UCSB IP address, you will also see a link to UC-e-Links, for jumping to the full text or catalogs or ILL request.

EndNote online full record, pt. 1

EndNote online full record, pt. 2

EndNote online full record, pt. 3

  • Above is an example of a full document record for a journal article from EndNote.  Note that the fields displayed will vary depending on the type of document and the information available when the record was entered
  • If you hover your cursor over a field in the full record, it becomes highlighted.  Click on the field to edit it. Note the link on the right-hand side of the screen that enables you to display currently empty fields for viewing and/or editing.
  • Note the magnifying glass by each author's name.  Clicking on it will search your EndNote Web files for that author.

Collecting References

  • Hovering the cursor over the Collect tab, or clicking on it displays the three options for adding records to your EndNote Web library: Online Search, New Reference and Import References.
  • The Online Search option allows you to search online databases using EndNote itself as the search interface.  I do not recommend this option for the following reasons:
    • Not all databases are available for searching through EndNote basic. That long, long list on the drop-down menu is composed mainly of library catalogs from universities around the world -- not usually a prime source for chemistry, biochemistry and other science and engineering searching.
    • Also note: in the vast majority of cases, the EndNote user interface will be less sophisticated and less powerful than the normal user interface of the index in question which may negatively impact your search results.
  • New Reference lets you create a reference record manually.  See below for a representative screen shot
  • Import References lets you take a downloaded answer set from an electronic database and import the entire group of records into EndNote
  • Note that Web of Science databases, including the WoS core collection, BIOSIS Citation Index and Derwent Innovations Index (as well as a handful from other vendors) allow you to export answer sets directly to EndNote, skipping the import step.

New References

  • This is the option for manually entering references.  Note the drop-down menu for Reference Type.  If you select a reference type, EndNote will display the fields that are most relevant for that reference type (journal artilce, patent, dissertation, etc.)  Note that there are separate reference types for articles and electronic articles, books and electronic books, etc. The screenshot below is the Generic record type.
  • Click on a field box to open it for entry.  In the example, I have filled several fields, and opened the Number of Volumes field for entry. When you have entered data, the Cancel and Save buttons will appear at the bottom of the screen.
  • Once saved, your new reference can be manipulated just like an imported reference.

EndNote Web new reference entry, part I
EndNote new reference entry, part II
EndNote Web new reference entry, part III

Importing References

  • The Import References option is used to bring in sets of references from downloaded files.  Note that most databases will have some sort of export option.  Choose the one most appropriate for exporting references to EndNote, and save the file.
  • The file window allow you to enter the name and location of the file you wish to import.  The Browse button lets you look through the directories available on your computer for the desired file.
  • The Import Options drop-down menu lets you specify which database and vendor you are importing from.  EndNote has extensive lists of possible database/vendor combinations - make sure you choose the one that corresponds to the answer set you are importing.  The Select Favorites link lets you create a list of the databases you use most frequently to save time.  If you have selected one or more "favorites", only those databases will show up in the drop-down menu.  If you need a different database, use the Select Favorites option to add it to your favorites list at least temporariy.
  • Note that many database vendors (including SciFinder and SciFinder-n) now allow you to export references as a .RIS file, so it's a good idea to have RefMan RIS on your favorites list.
  • The To: dropdown menu lets you select which of your EndNote Web folders you'd like the reference(s) to be placed in.  For creating folders, see the Organize section below.

EndNote Web import references screen

Organize References

  • Hovering your cursor over, or clicking on Organize reveals the organzing options: Manage My Groups, Others' Groups, Find Duplicates and Manage Attachments.
  • Manage My Groups allows you to add or delete groups, and, if desired, open up groups for sharing with other EndNote Web users.  To share a group, click the check box under Share, then click the Manage Sharing button.  From the next screen you can add or delete the e-mail addresses of thoe you wish to share references with.  Sharing may be "read-only" or "read and write". Note that you can have different sharing arrangements for each folder if desired.  In the example below, I've elected to share the "My Publications" folder from ResearcherID.  The "group" icon to the left of the folder name indicates that it's being shared.
  • Others' Groups is only relevant if other users have elected to share with you.
  • Find Duplicates searches your EndNote library to determine whether you have duplicate references entered.  If it detects them, you have the option to delete selected duplicates.
  • Manage Attachments refers to PDF copies of documents and other files attached to your EndNote records.  Note that your EndNote account has 2.0 gigabytes of storage space. If you are storing large files, like image files, or very  large PDFs (whole books or dissertations), this space can fill up quickly!

EndNote Web manage groups screen

Formatting References

  • Hovering your cursor over, or clicking on the Format tab displays the options: Bibliography, Cite While U Write Plug-In, Format Paper and Export References.
    • Bibliography lets you create stand-alone bibliographies from selected references in your EndNote library in a selected citation style (see below.)
    • Cite While U Write Plugin has links for downloading a plug-in (for either Windows or Mac OS) which links your EndNote library to Microsoft Word, allowing you to insert "live" footnotes into and bibliography into a Word document, which will, for example, automatically renumber footnotes if you rearrange your document. For more information on using Cite While U Write, see the EndNote tutorials or the Cite While U Write section of the UCSB Library's EndNote Desktop guide.
    • Format Paper allows you to take an RTF format document containing partial citations and convert it to fully formatted footnotes and bibliography using your chosen citation style from within  EndNote Web.  For more intfomation on using Format Paper, see the relevant EndNote help page.
    • Export References allows you to export selected references in a variety of file formats (EndNote, BibTeX, RefMan, Refer, and tab-delimited.)


  • This option allows you to save as a file (HTML, RTF or TXT), e-mail or print a formatted bibliography.
  • To use, first select the references in your EndNote library you wish to include using the upper drop-down menu.
  • Then, select the bibliopgraphic citation style you wish to follow.  Since there are hundreds of citation styles to choose from, it is advantageous to create a "favorites" list, using the "Select Favorites" option.  Once you have done so, only your "favorites" will appear in the main drop-down menu.  You can always add or delete favorites from your list by using the "Select Favorites" link.
  • Then, select the file format you wish to use, and click Save, E-Mail or Preview and Print.  It is usually a good idea to preview your bibliography before printing, e-mailing or saving it, to make sure you have the right references, are using the correct format and have all the requisite information in your records.

EndNote online create bibliography


  • When downloaded and installed to a computer with Microsoft Word, the Cite-While-You-Write plugin adds a menu item to the top menu bar in Word.  Note for Macintosh users:  You may need to go into the Preferences for Word and select EndNote online as opposed to EndNote.  If this is not done, the plugin will search for the EndNote desktop software on your computer, and, unable to find it, give you an error message.
  • Clicking on the EndNote Web menu tab will open a login screen.  Once you have logged into your EndNote online account, a new menu bar will become available.

EndNote CiteWhileUWrite menu bar for Microsoft Word for Windows

EndNote CiteWhileUWrite menu bar for Microsoft Word for Windows

  • While typing a document, the Insert Citations button will open a window allowing you to search your EndNote Web database and select a citation to insert.  It will appear in the style selected in the drop-down style menu.  Note that the style menu contains those styles which you have added to your Favorites list in EndNote onlne. You may search by author, year of publication or title keyword.  Select the desired citation and click Insert to enter the footnote and add the reference to the bibliography.

Cite-While-You-Write reference search

  • To change citation styles, simply select a new style from the dropdown menu.  If you edit the document (e.g. cutting and pasting sections), clicking the Update Citations and Bibliography link will rearrange and renumber (if necessary) both the citations and bibiliography.


  • Thisfeature does not relate directly to creating a database of bibliographic references.  Rather, it is designed to help scholarly authors select potential journals in which to publish their research.
  • When you click on the link, you are taken the Web of Science Master Journal List (see image below.)
  • To use Match, click on the Match Manuscript link  on the pMaster Journal List page. You will be prompted to create an account and log in. Your EndNote/Web of Science login and password also work here. If you came here from EndNote, you should already be logged in,and hitting the Login button will take you straight in.

EndNote Match opening screen

  • enter the title and abstract of your paper.  If you will be using references from your EndNote database for the paper, select the folder containing the references, and click Find Journals
  • Comparing your keywords and refeences to papers in the Web of Science database, the system will suggest likely journals. See example, below.  (Note: the journals suggested are *not* the journal in which the article was actually published!)

EndNote online Match entry screen

EndNote online Match results, pt. 1

EndNote online Match results, pt. 2

  • Links from this screen will take you to the journal's submission page, and/or to information about the journal from the publisher's website.
  • Results for a journal search are below.Note the firlter options similar to to those in Web of Science.

EndNote Match journal search results


EndNote downloads screen

  • CiteWhileUWrite has already been described above. Note the three different versions of the plug-in and make sure you choose the correct one for your computer.
  • Capture Reference is a drag-and-drop add-on for your Web Browser. I allows you to directly capture citations to Web pages to EndNote by simply clicking the installed button on your brower.
  • EndNote Click allows you to directly send downoaded PDFs to EndNote as attachments to records. Remember that 2.0 GB space limitation!


© 2024 Charles F. Huber

Creative Commons License
This work by Charles F. Huber is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
Based on a work at

Screenshots from EndNote online are copyright © 2018 by Clarivate Analytics.  Screenshots from Microsoft Word are © 2015 by the Microsoft Corporation.  All are used under fair use for educational purposes only.

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